Package: biomaRt

Version: 2.34.2

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings biomaRt_2.34.2.tar.gz

StartedAt: 2018-04-11 21:49:20 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:51:05 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 105.2 seconds

RetCode: 0

Status:  OK

CheckDir: biomaRt.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings biomaRt_2.34.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/biomaRt.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.34.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biomaRt’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::smartKeys’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: listEnsemblArchives.Rd:10: Dropping empty section \arguments
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
getBM  0.612  0.016  11.388
select 0.576  0.024  11.377
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

* installing *source* package ‘biomaRt’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomaRt)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(biomaRt)
> 
> test_check("biomaRt")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 9 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.324   0.056  13.961 

name	user	system	elapsed
NP2009code	0	0	0
attributePages	0	0	0
exportFASTA	0.000	0.000	0.001
filterOptions	0	0	0
filterType	0	0	0
getBM	0.612	0.016	11.388
getBMlist	0	0	0
getGene	0.000	0.000	0.001
getLDS	0	0	0
getSequence	0.000	0.000	0.001
getXML	0.000	0.000	0.001
listAttributes	0.000	0.000	0.001
listDatasets	0.004	0.000	0.000
listEnsembl	0.000	0.000	0.001
listEnsemblArchives	0.012	0.000	0.311
listFilters	0.004	0.000	0.001
listMarts	0.000	0.000	0.001
select	0.576	0.024	11.377
useDataset	0	0	0
useEnsembl	0	0	0
useMart	0.004	0.000	0.000